Finding Target Genes for DNA Binding Proteins

William J. Meilandt wmeiland at
Mon Sep 23 13:26:55 EST 1996

We have a putative DNA binding protein and would like to identify the 
genomic sequences to which the potein binds to.  Does any one have 
references or ideas they would like to share?

I am considering to purify the protein and put it on a column and then 
pass predigested genomic DNA thru the column to isolate genomic fragments 
which bind to my protein.  Is it better to used protein purified from my 
tissue of interest or in vitro translated?

An alternative approach would be to screen a genomic library with the 
putative binding site for the DNA-binding protein. Isolate this clone, 
digest it into smaller pieces, clone into a vector and re-screen with 
the binding site, and sequence the positive clones. 

Any suggestions on which method would work better, or if you know of a 
different method of isloating the targets of DNA-binding proteins,  
would greatly appreciated.    

Thank You

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